Level Up Your Reproducibility Game with Quarto

Bjorn and Claudiu

Bjørn Peare Bartholdy
Data Steward, Delft University of Technology

Claudiu Forgaci
Assistant Professor, Delft University of Technology

About Quarto

Quarto: What is it?

A free, open-source scientific and technical publishing system built on Pandoc.

Documents are authored using markdown.

Did I mention free and open source? 😎

Quarto Language support

Code can be seamlessly integrated in Quarto documents

Python
R
Julia
Observable

Quarto Output formats

Documents
- HTML
- PDF
- DOCX
- MD
- Jupyter
Presentations
- reveal.js
- beamer
- powerpoint

Books
- HTML
- PDF
- EPUB
- DOCX
- AsciiDoc
Websites
- HTML (Bootstrap 5)
- publish directly to Netlify

And many more.

Quarto Output formats

Documents
- HTML
- PDF
- DOCX
- MD
- Jupyter
Presentations
- reveal.js
- beamer
- powerpoint

Books
- HTML
- PDF
- EPUB
- DOCX
- AsciiDoc
Websites
- HTML (Bootstrap 5)
- publish directly to Netlify

And many more.

No, seriously, see the full list here

Quarto Extensions

Extensions by both developers and the community

shortcodes
- fontawesome
- social-embeds
- …
filters
- lightbox
- shinylive
- include-code-files
- …
formats
- letter-pdf
- rladies-revealjs
- blackboard-revealjs
- journal templates
- …

More extensions

Bring your own IDE

RStudio
VSCode
Neovim
Jupyter

Extensive documentation

Compared to existing options

RMarkdown for R users and Jupyter for Python users

Quarto is more streamlined and specifically tailored to scientific output

built-in functionality
- cross-refs
- author metadata
more output options
- including Jupyter

formatting features
- columns
- callouts
- footnotes

Note

I’m a callout

Compared to existing options

RMarkdown for R users and Jupyter for Python users

Quarto is more streamlined and specifically tailored to scientific output

built-in functionality
- cross-refs
- author metadata
more output options
- including Jupyter

formatting features
- columns
- callouts
- footnotes

Important

I’m an important callout

Compared to existing options

RMarkdown for R users and Jupyter for Python users

Quarto is more streamlined and specifically tailored to scientific output

built-in functionality
- cross-refs
- author metadata
more output options
- including Jupyter

formatting features
- columns
- callouts
- footnotes¹

Important

I’m an important callout

Active development

GIPHY

Quarto examples

Example projects

mintEMU

PhD dissertation

Example websites

R Café

Rbanism

Example presentation

You’re looking at it!

GIPHY

Join us

Join an upcoming R Café at TU Delft!

Join the Rbanism community for meet-ups, workshops, challenges and more around R in urbanism research!

We run these activities in close collaboration with the TU Delft Digital Competence Centre, TU Delft Research Data Services, Open Science Community Delft, and the Netherlands eScience Center.

The hands-on part (if you missed it)

Quarto: the basics

We’ll start out with a blank Quarto document (my-article.qmd)

First we need to populate the YAML header

---
title: Catchy title or pun: the actual title
author: Me and Al
---

Quarto: the basics

We’ll start out with a blank Quarto document (my-article.qmd)

Then add some markdown content

---
title: Catchy title or pun: the actual title
author: Me and Al
---

Quarto: the basics

We’ll start out with a blank Quarto document (my-article.qmd)

Then add some markdown content

---
title: Catchy title or pun: the actual title
author: Me and Al
---

## Introdution

This paper will make an important impact in a specific field of science, 
despite having "negative" results.

The aims of this paper are:

- something important
- some other important things
- maybe a few less important things

Quarto: the basics

Now render the document.

You can either render from your IDE,

or using the command line

quarto render my-article.qmd # defaults to html output
quarto render my-article.qmd --to pdf
quarto render my-article.qmd --to docx

Quarto: the basics

Dynamic variables- don’t repeat yourself!

metadata shortcode
{{< meta name-of-variable >}}

Include external content (e.g. qmd or md files)
{{< include name-of-file.ext >}}

Include custom variables from _variables.yml
{{< var name-of-variable >}}

Important

Using _variables.yml only works with Quarto projects

Otherwise you will get the error ?var:<varname>

Quarto: the basics

You can add keywords to the yaml header and include them in the text

---
title: Catchy title or pun: the actual title
author: Me and Al
---

## Introdution

This paper will make an important impact in a specific field of science, 
despite having "negative" results.

The aims of this paper are:

- something important
- some other important things
- maybe a few less important things

Quarto: the basics

You can add keywords to the yaml header and include them in the text

---
title: Catchy title or pun: the actual title
author: Me and Al
keywords: this; is; science!
---

{{< meta keywords >}}

## Introdution

This paper will make an important impact in a specific field of science, 
despite having "negative" results.

The aims of this paper are:

- something important
- some other important things
- maybe a few less important things

Quarto: the basics

And maybe you already wrote the materials and methods section,

which you have in another file called *_matmet.qmd*

---
title: Catchy title or pun: the actual title
author: Me and Al
keywords: this; is; science!
---

{{< meta keywords >}}

## Introdution

This paper will make an important impact in a specific field of science, 
despite having "negative" results.

The aims of this paper are:

- something important
- some other important things
- maybe a few less important things

{{< include _matmet.qmd >}}

Quarto: the basics

Of course the real power lies in seemlessly combining text and code (with output).

Using any of the supported languages, like R

---
title: Catchy title or pun: the actual title
author: Me and Al
keywords: this; is; science!
---

{{< meta keywords >}}

## Introdution

This paper will make an important impact in a specific field of science, 
despite having "negative" results.

The aims of this paper are:

- something important
- some other important things
- maybe a few less important things



{{< include _matmet.qmd >}}

Quarto: the basics

Of course the real power lies in seemlessly combining text and code (with output).

Using any of the supported languages, like R

---
title: Catchy title or pun: the actual title
author: Me and Al
keywords: this; is; science!
---

{{< meta keywords >}}

## Introdution

This paper will make an important impact in a specific field of science, 
despite having "negative" results.

The aims of this paper are:

- something important
- some other important things
- maybe a few less important things



{{< include _matmet.qmd >}}

## Results

```{r}
#| label: fig-airquality
#| fig-cap: "Temperature and ozone level."
#| warning: false
#| echo: true

library(ggplot2)

ggplot(airquality, aes(Temp, Ozone)) + 
  geom_point() + 
  geom_smooth(method = "loess")


```

Quarto: the basics

Of course the real power lies in seemlessly combining text and code (with output).

Using any of the supported languages, like R, or Python

---
title: Catchy title or pun: the actual title
author: Me and Al
keywords: this; is; science!
---

{{< meta keywords >}}

## Introdution

This paper will make an important impact in a specific field of science, 
despite having "negative" results.

The aims of this paper are:

- something important
- some other important things
- maybe a few less important things



{{< include _matmet.qmd >}}

## Results

```{python}
#| label: fig-polar
#| fig-cap: "A line plot on a polar axis"

import numpy as np
import matplotlib.pyplot as plt

r = np.arange(0, 2, 0.01)
theta = 2 * np.pi * r
fig, ax = plt.subplots(
  subplot_kw = {'projection': 'polar'} 
)
ax.plot(theta, r)
ax.set_rticks([0.5, 1, 1.5, 2])
ax.grid(True)
plt.show()


```

Quarto: the basics

Added bonus: built-in cross-referencing

---
title: Catchy title or pun: the actual title
author: Me and Al
keywords: this; is; science!
---

{{< meta keywords >}}

## Introdution

This paper will make an important impact in a specific field of science, 
despite having "negative" results.

The aims of this paper are:

- something important
- some other important things
- maybe a few less important things



{{< include _matmet.qmd >}}

## Results

```{python}
#| label: fig-polar
#| fig-cap: "A line plot on a polar axis"

import numpy as np
import matplotlib.pyplot as plt

r = np.arange(0, 2, 0.01)
theta = 2 * np.pi * r
fig, ax = plt.subplots(
  subplot_kw = {'projection': 'polar'} 
)
ax.plot(theta, r)
ax.set_rticks([0.5, 1, 1.5, 2])
ax.grid(True)
plt.show()


```

Blah, blah, blah, something important. Don't believe me? Check out @fig-polar!

Quarto: the basics

---
title: Catchy title or pun: the actual title
author: Me and Al
keywords: this; is; science!
---

{{< meta keywords >}}

## Introdution

This paper will make an important impact in a specific field of science, 
despite having "negative" results.

The aims of this paper are:

- something important
- some other important things
- maybe a few less important things

{{< include _matmet.qmd >}}

## Results

```{python}
#| label: fig-polar
#| fig-cap: "A line plot on a polar axis"

import numpy as np
import matplotlib.pyplot as plt

r = np.arange(0, 2, 0.01)
theta = 2 * np.pi * r
fig, ax = plt.subplots(
  subplot_kw = {'projection': 'polar'} 
)
ax.plot(theta, r)
ax.set_rticks([0.5, 1, 1.5, 2])
ax.grid(True)
plt.show()
```
Blah, blah, blah, something important. Don't believe me? Check out @fig-polar!

## Conclusion

Quarto is awesome!

Play around in the sandbox
See the R and Python outputs